Freesurfer November 2014

freesurfer@nmr.mgh.harvard.edu

99 participants
144 discussions

Re: [Freesurfer] adding insula voxels
by Adam Mezher 06 Nov '14

06 Nov '14

I uploaded one when I sent the first email, did you receive it? Uploaded to: ftp.nmr.mgh.harvard.edu ; cd transfer/incoming The file was titled ‘mezher_insula_fail.tar.gz’ which contains the entire FS folder for one subject. Should I go ahead and resend it? Thanks!

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notal-check/pial edits
by Octavian Lie 06 Nov '14

06 Nov '14

Dear All, this is very basic. I have Analyze volumes, and I was suggested to use -notal-check to bypass the 3rd recon step. I wanted to make sure skipping the T registration step would not have the potential to mess up the spherical registration in autorecon3 in any way on a case by case basis. I do not want to spend time in tkregister2 unless is necessary for the spherical registration step. Also, I anticipate losts of pial edits (let's exclude the wm edits/cp), and I wanted to make sure different command scenarios are correct: 1. recon-all -autorecon1 -subjid edit pia, save brainmask.mgz recon-all -autorecon2 -autorecon3 -subjid 2. recon-all -autorecon1 -autorecon2 -subjid edit pia, save brainmask.mgz recon-all -autorecon2-pial -autorecon3 -subjid (preferred) 3. recon-all -subjid edit pia, save brainmask.mgz recon-all -autorecon-pial -subjid Please comment, thank you, Octavian

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Generating T1 + Aseg views without Tkmedit and Freeview
by Pedro Paulo de Magalhães Oliveira Junior 06 Nov '14

06 Nov '14

I'm sorry if this has been answered before, I have browsed the mailing and found nothing answering this. I need to generate three views of the T1 data superimposed with Aseg data automatically for Quality Control without using FreeView or Tkmedit (the server generating this has no X11) Is it possible to do it with the command line tools? Thanks --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441

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Crash on recon-all on Macbook Pro (Mavericks and Yosemite)
by Matthew Riddle 06 Nov '14

06 Nov '14

Dear Freesurfer Team, I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I’m still experiencing an issue with freesurfer that I’m hoping you might have some idea about. Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal: sudo –E recon-all –s bert –all The processes crashes in a minute or two at the same place each time, and this is the last bit of output. MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014 I tried this on an almost identical machine running Mavericks, and got the exact same problem. >From my bugr output: FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.0.0 x86_64 The recon-all.log file doesn’t provide any additional information, it just mirrors the output from the terminal. Thanks, -Matt

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mris_preproc error
by Cooke, Gillian 05 Nov '14

05 Nov '14

Hi All, I am getting a consistent error when I try to run mris_preproc - I'm baffled as I've used all of my scripts and fsgd files before. There are 2 groups with 3 covariates but I keep getting this error: mris_preproc --fsgd fsgd/HRR60.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out mris_preproc/lh.HRR60.thickness.10.mgh ERROR: no subjects specified But my fsgd file lists all subject numbers: GroupDescriptorFile 1 Title ACCE HRR60 Class Control Class Cancer Variables Age_demeaned Ed_demeaned HRR60 Input 505_1 Cancer -5.63 1.5 43 Input 506_1 Cancer 7.37 3.5 53 Input 509_1 Cancer 4.37 -0.5 44 Input 517_1 Cancer -20.63 -1.5 38 Input 518_1 Cancer -4.63 -2.5 35 Input 520_1 Cancer 0.37 1.5 37 Input 521_1 Control 3.37 1.5 49 Input 524_1 Cancer 3.37 -0.5 32 Input 525_1 Control -12.63 -2.5 51 #Input 528_1 Cancer 10.37 3.5 Input 529_1 Control -28.63 4.5 32 Input 530_1 Cancer 1.37 1.5 24 Input 531_1 Cancer 6.37 7.5 55 Input 532_1 Cancer -1.63 1.5 14 Input 533_1 Cancer -10.63 3.5 36 Input 534_1 Control -3.63 1.5 25 Input 536_1 Control -11.63 0 47 Input 547_1 Control 10.37 1.5 25 Input 548_1 Control -18.63 -0.5 46 Input 549_1 Cancer -21.63 -0.5 38 Input 554_1 Control -21.63 -0.5 38 Input 558_1 Cancer 9.37 -1.5 24 Input 563_1 Control 0.37 0.5 30 Input 564_1 Control 7.37 1.5 14 Any help is greatly appreciated! Gill _____________________ Gillian Cooke, Ph.D. Postdoctoral Research Associate Lifelong Brain & Cognition Lab Decision Neuroscience Lab Beckman Institute University of Illinois, Urbana

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Infinite loop in mri_convert
by Nooshin Zadeh 05 Nov '14

05 Nov '14

Dear FreeSurfer experts, I get a new message when I use "mri_convert" command to convert dicom to mgz. I used to apply this command before and there was no problem. I wonder what is the reason that I get the new message. In addition, it does not create mgz file, and goes to infinite loop. *mri_convert "/M1/t1_se_ax_5/IM-0004-0001.dcm" "/FS/M1/mri/orig/001.mgz"* mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /M1/t1_se_ax_5/IM-0004-0001.dcm... Getting Series No Scanning Directory INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5 INFO: Scanning for Series Number 5INFO: found 37 files in series INFO: loading series header info. I appreciate if you can advise me. Regards, Nooshin PhD Candidate Departments of Electrical & Computer Engineering University of Miami Email: n.zadeh(a)miami.edu

2 1

Freeview-stable4 error?
by DeCross, Stephanie N. 05 Nov '14

05 Nov '14

Hi, I'm trying to look at 2 connectivity files (saved in SPM) at the same time using Freeview, but how I've been doing it in the past is no longer working and I haven’t changed anything on my end. What I had been doing: 1. cd to the folder with my connectivity files and typing the shortcut command: stable4 (which does the following: setenv USE_STABLE_4_5_0; source /space/freesurfer/nmr-stable4-env) 2. typing the command: freeview ../../../../N12Trio_avg152T1.nii LSHSxAmyg.covBDI_PosCorr_p05_20vox.img LSHSxAmyg.covBDI_NegCorr_p05_20vox.img_blue.nii.gz This command used to work fine, but is now giving me the error: freeview.bin: error while loading shared libraries: libvtkverdict.so.vtk5.2.0: cannot open shared object file: No such file or directory This command DOES work if I don't type the shortcut command stable4 and instead keep using the stable53 environment I was already in (setenv FSL_DIR /usr/pubsw/packages/fsl/4.1.9; source /space/nexus/1/users/avi-tools/enable_avi.csh; setenv SUBJECTS_DIR /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53; source /usr/local/freesurfer/nmr-stable53-env). While I'm not positive it affects anything, I'd rather be consistent with the stable4 way I've been doing it in the past - is there a way to fix it and use Freeview in stable4, or does this freeview.bin error mean that I can no longer use Freeview with stable4? Thanks, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078

2 1

freeview fault: PETSC Error ...
by Krieger, Donald N. 04 Nov '14

04 Nov '14

I recently downloaded and installed freesurfer-Linux-centos6_x86_64-table-pub-v5.3.0.tar.gz . I had been running this version previously but had to reload everything due to a disk crash. recon-all -all goes to completion with no errors. freeview starts up fine but fails on loading a volume file with the PETC error listed below. I found several references to this error in the archive but no resolution for my problem. Any thoughts would be welcome - thanks. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named BTRC-Server01 by kriegerd Tue Nov 4 06:55:17 2014 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 Regards, Don [Signature0001] Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text

2 1

Create surface Labels of equal size
by Bastian Cheng 04 Nov '14

04 Nov '14

Dear Freesurfers, I would like to mark the brain surface (fsaverage) for an illustration of stimulation areas (TMS). I have calculated coordinates in Vertex RAS and Vertex Talairach. They are correctly located on the fsaverage surface in tksurfer. Is there a way to create labels of equal sizes at those coordinates? Ideally by using a script (since I have to mark them in 50 patients). this is purely for illustrative purposes. All coordinates are in fasaverage space. Any help would be appreciated, Bastian

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Recon-all error on 1.5t GE T1
by Zachary Greenberg 04 Nov '14

04 Nov '14

Hi Freesurfers, I'm trying to recon-all a T1 image acquired on a 1.5T GE scanner. I'm running: recon-all -subjid EC -all -mprage -openmp 8 -use-gpu And the process errors out at: mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz mghRead(/crtx1/zgreenberg/subjects/EC/mri/aseg.auto.mgz, -1): read error Apparently there is some error trying to read aseg.auto.mgz during mri_seg_diff. Has anyone had this problem before? I tried to mdi_info aseg.auto.mgz and I get the same read error. Thanks for any help you can offer. Log and error attached. -zack

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Freesurfer November 2014